graphlan_import: import2graphlan.xml annotate

annotate import2graphlan.xml @ 42:fa2bd894219f draft

Uploaded

author	george-weingart
date	Sat, 06 Sep 2014 13:45:33 -0400
parents	34a1b347e2e7
children	c5c1037078e5

rev	line source
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	1 <tool id="import2graphlan" name="import2graphlan" version="1.0.0">
25 9ecf8701f72f Uploaded george-weingart parents: 23 diff changeset	2 <description>Import to Graphlan</description>
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	3 <command interpreter="python">
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	4 export2graphlan.py
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	5 -i $inp_data
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	6 -o $out_data
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	7 -t $output_tree_file
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	8 -a $output_annot_file
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	9
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	10 --annotations $export_annotations
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	11 --external_annotations $export_external_annotations
37 233b2e67d6ea Uploaded george-weingart parents: 36 diff changeset	12 --background_levels $background_levels
38 c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	13
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	14
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	15 #if $str($gchoice.global_choice) == "a":
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	16
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	17 #if $str($gchoice.background_clades) != " ":
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	18 --background_clades $gchoice.background_clades
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	19 #end if
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	20 #if $str($gchoice.background_colors) != " ":
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	21 --background_colors $gchoice.background_colors
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	22 #end if
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	23
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	24 #if $str($gchoice.export_title) != " ":
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	25 --title $gchoice.export_title
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	26 #end if
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	27
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	28
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	29
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	30
38 c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	31 --title_font_size $gchoice.title_font_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	32 --def_clade_size $gchoice.def_clade_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	33 --min_clade_size $gchoice.min_clade_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	34 --max_clade_size $gchoice.max_clade_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	35 --def_font_size $gchoice.def_font_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	36 --min_font_size $gchoice.min_font_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	37 --max_font_size $gchoice.max_font_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	38 --annotation_legend_font_size $gchoice.annotation_legend_font_size
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	39 --abundance_threshold $gchoice.abundance_threshold
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	40 --least_biomarkers $gchoice.least_biomarkers
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	41
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	42 #if $str($gchoice.discard_otus ) == "1":
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	43 --discard_otus
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	44 #end if
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	45 #end if
38 c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	46
c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	47
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	48
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	49 --skip_rows 1,2
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	50 </command>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	51
29 3b2b6c5e38e2 Uploaded george-weingart parents: 27 diff changeset	52 <inputs>
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	53 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse" help="This is the file that was used as input for Lefse"/>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	54 <param format="lefse_internal_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/>
29 3b2b6c5e38e2 Uploaded george-weingart parents: 27 diff changeset	55 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
3b2b6c5e38e2 Uploaded george-weingart parents: 27 diff changeset	56 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
37 233b2e67d6ea Uploaded george-weingart parents: 36 diff changeset	57 <param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>
30 b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	58
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	59 <conditional name="gchoice">
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	60 <param name="global_choice" type="select" label="Select Global Choices" help="Select choices">
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	61 <option value="d" selected='True'>Default</option>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	62 <option value="a">Advanced</option>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	63 </param>
38 c670bf87b733 Uploaded george-weingart parents: 37 diff changeset	64
30 b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	65 <when value="a">
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	66 <param name="background_clades" type="text" format="text" label="Background Clades" value=" " />
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	67 <param name="background_colors" type="text" format="text" label="Background Colors" value=" " />
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	68 <param name="export_title" type="text" format="text" label="Title" value=" "/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	69 <param name="title_font_size" type="integer" size="4" value="15" label="Title font size"/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	70 <param name="def_clade_size" type="integer" size="4" value="0" label="Default Clade size"/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	71 <param name="min_clade_size" type="integer" size="4" value="20" label="Minimum Clade size that are Biomarkers"/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	72 <param name="max_clade_size" type="integer" size="4" value="200" label="Maximum Clade size that are Biomarkers"/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	73 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	74 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	75 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	76 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	77 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	78 <param name="most_abundant" type="integer" size="4" value="0" label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	79 <param name="least_biomarkers" type="integer" size="4" value="0" label="Minimum number of biomarkers to extract "/>
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	80 <param name="discard_otus" type="select" label="If specified the OTU ids will be discarded from the taxonomy" value="0" >
41 34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	81 <option value="0">No</option>
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	82 <option value="1">Yes</option>
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	83 </param>
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	84
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	85
c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	86
30 b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	87 </when>
b4fb4d403061 Uploaded george-weingart parents: 29 diff changeset	88 </conditional>
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	89 </inputs>
29 3b2b6c5e38e2 Uploaded george-weingart parents: 27 diff changeset	90 <outputs>
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	91 <data name="output_annot_file" format="circl" />
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	92 <data name="output_tree_file" format="circl" />
29 3b2b6c5e38e2 Uploaded george-weingart parents: 27 diff changeset	93 </outputs>
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	94
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	95 <help>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	96 Overview
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	97 ========
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	98 export2graphlan is an OPTIONAL tool that automatically convert LEfSe, MetaPhlAn2, and HUMAnN input and/or output files, to GraPhlAn. Input file can be also given in BIOM (both 1 and 2) format.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	99
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	100 The aim of this tool is to support biologists, helping them by provide the tree and the annotation file for GraPhlAn, automatically.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	101
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	102 Input files
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	103 ===========
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	104
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	105 As shown in the image below, export2graphlan can work with just one of the following files or with both of them.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	106
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	107 * Result of MetaPhlAn or HUMAnN analysis: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	108
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	109 * Output of LEfSe: This file is the result of LEfSe execute on the Result of MetaPhlAn or HUMAnN analysis file. This file allow GraPhlAn to highlight for you the found biomarkers.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	110
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	111 Input parameters
41 34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	112 ================
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	113
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	114 --annotations ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None
41 34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	115
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	116 --external_annotations EXTERNAL_ANNOTATIONS
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	117 List which levels should use the external legend for the annotation. Use a comma separate values form,
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	118
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	119 e.g., --annotation_levels 1,2,3. Default is None
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	120
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	121 --background_levels BACKGROUND_LEVELS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	122 List which levels should be highlight with a shaded
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	123 background. Use a comma separate values form, e.g.,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	124 --background_levels 1,2,3
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	125
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	126 --background_clades BACKGROUND_CLADES
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	127 Specify the clades that should be highlight with a shaded background. Use a comma separate values form and surround the string with " if it contains spaces.
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	128 Example: --background_clades "Bacteria.Actinobacteria,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	129 Bacteria.Bacteroidetes.Bacteroidia,
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	130 Bacteria.Firmicutes.Clostridia.Clostridiales"
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	131
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	132 --background_colors BACKGROUND_COLORS
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	133 Set the color to use for the shaded background. Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()) format.
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	134
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	135 Use a comma separate values form and surround the string with " if it contains spaces.
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	136
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	137 Example:
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	138 --background_colors "#29cc36, (150; 100; 100), (280;
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	139 80; 88)"
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	140
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	141 --title TITLE If specified set the title of the GraPhlAn plot.
42 fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	142
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	143 Surround the string with " if it contains spaces, e.g., --title "Title example"
fa2bd894219f Uploaded george-weingart parents: 41 diff changeset	144
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	145 --title_font_size TITLE_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	146 Set the title font size. Default is 15
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	147 --def_clade_size DEF_CLADE_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	148 Set a default size for clades that are not found as
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	149 biomarkers by LEfSe. Default is 10
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	150 --min_clade_size MIN_CLADE_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	151 Set the minimum value of clades that are biomarkers.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	152 Default is 20
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	153 --max_clade_size MAX_CLADE_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	154 Set the maximum value of clades that are biomarkers.
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	155 Default is 200
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	156 --def_font_size DEF_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	157 Set a default font size. Default is 10
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	158 --min_font_size MIN_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	159 Set the minimum font size to use. Default is 8
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	160 --max_font_size MAX_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	161 Set the maximum font size. Default is 12
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	162 --annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	163 Set the font size for the annotation legend. Default
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	164 is 10
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	165 --abundance_threshold ABUNDANCE_THRESHOLD
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	166 Set the minimun abundace value for a clade to be
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	167 annotated. Default is 20.0
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	168 --most_abundant MOST_ABUNDANT
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	169 When only lefse_input is provided, you can specify how
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	170 many clades highlight. Since the biomarkers are
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	171 missing, they will be chosen from the most abundant
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	172 --least_biomarkers LEAST_BIOMARKERS
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	173 When only lefse_input is provided, you can specify the
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	174 minimum number of biomarkers to extract. The taxonomy
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	175 is parsed, and the level is choosen in order to have
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	176 at least the specified number of biomarkers
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	177 --discard_otus If specified the OTU ids will be discarded from the
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	178 taxonmy. Default behavior keep OTU ids in taxonomy
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	179 --internal_levels If specified sum-up from leaf to root the abundances
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	180 values. Default behavior do not sum-up abundances on
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	181 the internal nodes
25 9ecf8701f72f Uploaded george-weingart parents: 23 diff changeset	182
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	183
41 34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	184 Input data matrix parameters
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	185 ============================
39 c4ffb0c51836 Uploaded george-weingart parents: 38 diff changeset	186
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	187 --sep SEP
41 34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	188
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	189 --out_table OUT_TABLE : This is where to write the processed data matrix to file
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	190
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	191 --fname_row FNAME_ROW : Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	192
41 34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	193 --sname_row SNAME_ROW column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	194
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	195 --metadata_rows METADATA_ROWS Row numbers to use as metadata[default None, meaning no metadata
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	196
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	197 --skip_rows SKIP_ROWS Row numbers to skip (0-indexed, comma separated) from the input file[default None, meaning no rows skipped
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	198
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	199 --sperc SPERC Percentile of sample value distribution for sample selection
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	200
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	201 --fperc FPERC Percentile of feature value distribution for sample selection
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	202
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	203 --stop STOP Number of top samples to select (ordering based on percentile specified by --sperc)
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	204
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	205 --ftop FTOP Number of top features to select (ordering based on percentile specified by --fperc)
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	206
34a1b347e2e7 Uploaded george-weingart parents: 40 diff changeset	207 --def_na DEF_NA Set the default value for missing values [default None which means no replacement]
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	208
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	209 Integration
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	210 ===========
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	211
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	212 A graphical representation of how export2graphlan can be integrated in the analysis pipeline:
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	213
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	214 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	215 :height: 672
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	216 :width: 800
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	217
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	218 Want to know more?
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	219 ==================
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	220
27 252c242518f2 Uploaded george-weingart parents: 26 diff changeset	221 If you want to know more about export2graphlan please have a look at the tutorial `here`_
26 4c76917ae3d7 Uploaded george-weingart parents: 25 diff changeset	222
4c76917ae3d7 Uploaded george-weingart parents: 25 diff changeset	223
27 252c242518f2 Uploaded george-weingart parents: 26 diff changeset	224 .. _here: https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial
23 01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	225 </help>
01ba9f83f9a7 Renamed the function to import rather than export george-weingart parents: diff changeset	226 </tool>

Mercurial > repos > george-weingart > graphlan_import

annotate import2graphlan.xml @ 42:fa2bd894219f draft